Download Final Exam (Set B)

Final Exam (Set B) for Molecular Biology
(Spring 2008)
Instructors: Profs. YX Chen and JY Yang
1. Which of the following is not a polysaccharide?
A. chitin
B. amylopectin
C. glycosaminoglycan
D. glycerol
2. The sequence 5’-AGTCTGACT-3’ in DNA is equivalent to which sequence in
RNA?
A. 5’-AGUCUGACU-3’
B. 5’-UGTCTGUTC-3’
C. 5’-UCAGUCUGA-3’
D. 5’-AGUCAGACU-3’
3. Denaturation of double stranded DNA involves….
A. breakage into short double-stranded fragments.
B. separation into single strands.
C. hydrolysis of the DNA backbone.
D. cleavage of the bases from the sugar-phosphate backbone.
4. Weak chemical interactions are essential in the biological system. Which of
the following statement about weak chemical interaction is NOT TRUE?
A. Van der Waals forces and hydrogen bonds are all weak chemical
interactions.
B. Weak bonds are constantly made and broken at physiological temperature.
C. Hydrophobic interactions stabilize macromolecules.
D. Covalent bonds are the important forces for protein-protein interaction.
5. RNA can fold up to complex tertiary structure because
A. RNA chain is usually single-stranded and form long-range interactions in
addition to local double helical structure.
B. RNA contains ribose and uracil.
C. Some RNAs are enzymes.
D. RNA can form pseudoknot structure.
6. Which of the following is common to both E.coli and eukaryotic
chromosomes?
A. the DNA is circular.
B. the DNA is packaged into nucleosomes.
C. the DNA is contained in the nucleus.
D. the DNA is negatively supercoiled.
7. In what region of the interphase chromosome does transcription take place?
A. the telomere.
B. the centromere.
C. euchromatin.
D. heterochromatin
8. In prokaryotes, the lagging strand primers are removed by…
A. 3’ to 5’exonuclease.
B. DNA ligase.
C. DNA polymerase I.
D. DNA polymerase III.
9. Which one of the following statements about transcription in E.coli is true?
A. loose binding of the RNA polymerase core enzyme to DNA is nonspecific and unstable.
B. σ factor dramatically increases the relative affinity of the enzyme for
correct promoter sites.
C. almost all RNA start sites consist of a purine residue, with A being more
common than G.
D. all promoters are inhibited by negative supercoiling.
E. terminators are often A-U hairpin structures.
10. Which one of the following statements is incorrect?
A. there are two α subunits in the E.coli RNA polymerase.
B. there are one β subunit in the E.coli RNA polymerase.
C. E.coli has one sigma factor.
D. the β subunit of the E.coli RNA polymerase is inhibited by rifampicin.
E. the streptolydigins inhibit transcription elongation.
F. heparin is a polyanion, which binds to the β’ subunit.
11. Which two of the following statements about transcription are correct?
A. RNA synthesis occurs in the 3’ to 5’ direction.
B. the RNA polymerase enzyme moves along the sense strand of the DNA in
a 5’ to 3’ direction.
C. the RNA polymerase enzyme moves along the template strand of the
DNA in a 5’ to 3’ direction.
D. the transcribed RNA is complementary to the template strand.
E. the RNA polymerase adds ribonucleotides to the 5’ end of the growing
RNA chain.
F. the RNA polymerase adds deoxyribonucleotides to the 3’ end of the
growing RNA chain.
12. Which one of the following statements about the trp operon is true?
A. the RNA product of the trp operon is very stable.
B. the Trp repressor is a product of the trp operon.
C. the Trp repressor, like the Lac repressor, is a tetramer of identical subunits.
D. the Trp repressor binds to tryptophan.
E. tryptophan activates expression from the trp operon.
F. the trp operon is only regulated by the Trp repressor.
13. Which two of the following statements about sigma factors are false?
A. the E.coli RNA polymerase core enzyme cannot start transcription from
promoters in the absence of a sigma factor subunit.
B. different sigma factors may recognize different sets of promoters.
C. sigma factors recognize both the -10 and -35 promoter elements.
D. heat shock promoters in E.coli have different -35 and -10 sequences and
bind to a diverse set of 17 heat shock sigma factors.
E. sporulation in B.subtilis is regulated by a diverse set of sigma factors.
F. bacteriophage T7 expresses its own set of sigma factors as an alternative
to encoding its own RNA polymerase.
14. Which two of the following statements about RNA PolⅠgenes are true?
A. RNA PolⅠtranscribes the genes for ribosomal RNAs.
B. human cells contain 40 clusters of five copies of the rRNA gene.
C. the 18S, 5.8S and 28S rRNAs are synthesized as separate transcripts.
D. RNA PolⅠtranscription occurs in the nucleoplasm.
E. RNA PolⅠtranscription occurs in the cytoplasm.
F. rRNA gene clusters are known as nucleolar organizer regions.
15. Which two of the following statements about RNA Pol Ⅲ genes are true?
A. the transcriptional control regions of tRNA genes lie upstream of the start
of transcription.
B. highly conserved sequences in tRNA genes coding regions are also
promoter sequences.
C. TFⅢC contains TBP as one of its subunits.
D. TFⅢB is a sequence specific transcription factor on its own.
E. in humans 5S rRNA genes are arranged in a single cluster of 2000 copies.
16. Which one of the following statements about general transcription factors is
false?
A. TFⅡD binds to the TATA box.
B. TFⅡD is a multiprotein complex consisting of TBP and TAFⅡs.
C. TBP is a common factor in transcription by RNA PolⅠ,Ⅱand Ⅲ.
D. TFⅡB stabilizes the TFⅡD-DNA complex.
E. TFⅡE, TFⅡH and TFⅡJ associate with the transcription complex after
RNA polymerase binding.
F. TFⅡH phosphorylates the CTD.
17. Which one of the following statements correctly describes initiation of
protein synthesis in E. coli?
A. the initiator tRNA binds to the Shine-Dalgarno sequence
B. three initiation factors are involved and IF2 binds to GTP.
C. the intermediate containing IF1, IF2, IF3, initiator tRNA and mRNA is
called the 30S initiation complex.
D. binding of the 50S subunit releases IF1, IF2, GMP and PPi.
E. the initiation process is complete when the 70S initiation complex is
formed which contains the initiator tRNA in the A site of the ribosome
and an empty P site.
18. E. coli release factor 1 (RF1) recognizes which codons?
A. UAA only.
B. UAG only.
C. UGA and UAA.
D. UAG and UAA.
E. UAG and UGA.
19. Which of the following protein synthesis factors are not equivalent pairs in
prokaryotes and eukaryotes?
A. EF-G; eEF2.
B. EF-Tu; eEF1α.
C. RF1 and RF3; eRF.
D. EF-Ts; eEFαβ.
20. The fact that most amino acids are specified by multiple codons is known as:
A. the “wobble” phenomenon.
B. the universality of the genetic code.
C. codon bias.
D. the anticodon hypothesis.
E. the redundancy of the genetic code.
21. List three differences between prokaryotic and eukaryotic translation (ignore
differences in ribosome structure).
22. Suppose that you are making use of the alternating copolymer
GUGUGUGUGU... as an mRNA in an in-vitro protein-synthesizing system.
Assuming that an AUG start coden is not needed in the in-vitro system, what
peptides are made by this mRNA? Write down the two RNA sequences that
could conceivably result from complete transcription of a DNA molecule that
has the following sequence in on of the strands – 5’-AGCTGCAATG-3’.
23. What are differences between a nucleosome,a core particle, and an octameric
disc? Which directly involve the histone H1?
24. Suppose a hyperthetical enzyme contains 156 amino acids. Assume amino
acid 28, which is a glutamic acid, is replaced in a mutant by asparagine and
as a result, all the enzyme activity is lost. Suppose in this mutant protein,
amino acid 76, which is asparagine, is replaced by glutamic acid and full
activity of the enzyme is restored. What can you say about amino acid 28 and
amino acid 76 in the normal protein?
25. A hyperthetical transposon has inserted at the target sequence 5’TTAGCA3’. Its left inverted repeat sequence is 5’-GCAATGGCA-3’. This now serves
as the donor molecule for a transposition event to the new target sequence
5’GATCCA-3’, in a recipient molecule. Show the structure of the DNA (both
strands) of the following molecules after all steps of transposition. (Assume
that the inverted repeats on the transposon are perfect).
A. The recipient molecule.
B. The donor molecule if transposition occurred by conservative pathway
C. The donor molecule if transposition occurred by the replicative pathway.
26. List several mechanisms a cell (eukaryotic) uses to increase the concentration
of a particular mRNA molecule to a very high level.
27. Give the two types of splicing that can occur in the processing of eukaryotic
mRNA, and state the difference
28. Explain and distinguish the roles of Shine-Dalgano sequence and Kozak
sequence in the regulation of gene expression.
29. What distinguishes negative regulation from positive regulation? How would
you distinguish negative and positive autoregulation?
30. List several epigenetic mechanisms that affect gene expression
31. What is a CpG island and what role it plays in gene regulation?
32. Explain insertional inactivation.
33. Once a series of recombinant plasmids or phages have been produced,
describe several ways in which plasmids or phages containing a particular
insert many be identified.